OMOP/Documentation/StandardizedVocabularies/VOCABULARY.md

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OMOP Common Data Model v5.1 Specifications
Authors: Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan, Clair Blacketer
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3.2 VOCABULARY

The VOCABULARY table includes a list of the Vocabularies collected from various sources or created de novo by the OMOP community. This reference table is populated with a single record for each Vocabulary source and includes a descriptive name and other associated attributes for the Vocabulary.

Field Required Type Description
vocabulary_id Yes varchar(20) A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit.
vocabulary_name Yes varchar(255) The name describing the vocabulary, for example "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" etc.
vocabulary_reference Yes varchar(255) External reference to documentation or available download of the about the vocabulary.
vocabulary_version Yes varchar(255) Version of the Vocabulary as indicated in the source.
vocabulary_concept_id Yes integer A foreign key that refers to a standard concept identifier in the CONCEPT table for the Vocabulary the VOCABULARY record belongs to.

Conventions

  • There is one record for each Vocabulary. One Vocabulary source or vendor can issue several Vocabularies, each of them creating their own record in the VOCABULARY table. However, the choice of whether a Vocabulary contains Concepts of different Concept Classes, or when these different classes constitute separate Vocabularies cannot precisely be decided based on the definition of what constitutes a Vocabulary. For example, the ICD-9 Volume 1 and 2 codes (ICD9CM, containing predominantly conditions and some procedures and observations) and the ICD-9 Volume 3 codes (ICD9Proc, containing predominantly procedures) are realized as two different Vocabularies. On the other hand, SNOMED-CT codes of the class Condition and those of the class Procedure are part of one and the same Vocabulary. Please refer to the Standardized Vocabularies specifications for details of each Vocabulary.
  • The vocabulary_id field contains an alphanumerical identifier, that can also be used as the abbreviation of the Vocabulary name.
  • The record with vocabulary_id = 'None' is reserved to contain information regarding the current version of the Entire Standardized Vocabularies.
  • The vocabulary_name field contains the full official name of the Vocabulary, as well as the source or vendor in parenthesis.
  • Each Vocabulary has an entry in the CONCEPT table, which is recorded in the vocabulary_concept_id field. This is for purposes of creating a closed Information Model, where all entities in the OMOP CDM are covered by a unique Concept.
  • In past versions of the VOCABULARY table, the vocabulary_id used to be a numerical value. A conversion table between these old and new IDs is given below:
Previous VOCABULARY_ID Version 5 VOCABULARY_ID
0 None
1 SNOMED
2 ICD9CM
3 ICD9Proc
4 CPT4
5 HCPCS
6 LOINC
7 NDFRT
8 RxNorm
9 NDC
10 GPI
11 UCUM
12 Gender
13 Race
14 Place of Service
15 MedDRA
16 Multum
17 Read
18 OXMIS
19 Indication
20 ETC
21 ATC
22 Multilex
24 Visit
28 VA Product
31 SMQ
32 VA Class
33 Cohort
34 ICD10
35 ICD10PCS
36 Drug Type
37 Condition Type
38 Procedure Type
39 Observation Type
40 DRG
41 MDC
42 APC
43 Revenue Code
44 Ethnicity
45 Death Type
46 Mesh
47 NUCC
48 Specialty
49 LOINC
50 SPL
53 Genseqno
54 CCS
55 OPCS4
56 Gemscript
57 HES Specialty
58 Note Type
59 Domain
60 PCORNet
61 Obs Period Type
62 Visit Type
63 Device Type
64 Meas Type
65 Currency
66 Relationship
67 Vocabulary
68 Concept Class
69 Cohort Type
70 ICD10CM